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View Full Text-PDF Int.J.Curr.Res.Aca.Rev.2017; Special Issue-4: 1-18 International Journal of Current Research and Academic Review ISSN: 2347-3215 Special Issue-4 (October-2017) Journal home page: http://www.ijcrar.com Molecular Interaction Analysis of Mutant H-Ras P21 against Phyllanthus emblica G. Shoba*, A. S. Pavithra and S. Ananthi Department of Biochemistry & Bioinformatics, Dr. MGR. Janaki College of arts and science, Chennai, Tamil Nadu, India *Corresponding author KEYWORDS ABSTRACT Malignant melanoma, Phyllanthus emblica Linn is widely used for medicinal purpose, usually from the plant, fresh (or) dried fruits are used. There are many bioactive compounds including H-Ras p21, Molecular docking, MAP Kinase apigenin, gallic acid, ellagic acid, chebulinic acid, quercetin, chebulagic acid, corilagin, isostrictiniin, methylg allate, luteolin, emblicanin A, emblicanin B, phyllaemblicin B, punigluconin and pedunculagin are tannins in Phyllanthus emblica. P.emblica possess several biological effects such as anticancer, antifungal, antiulcerogenic, antioxidant, and antidepressant and so on. The activation of Ras/Mitogen Activated Protein (MAP) kinase in turn deactivates MEK, a member of the MAPK signalling cascade. The GTP-bound mutant form H-Ras (Harvey-Ras) protein are found in 30% of human tumors and caused due to point mutation at position 12, 13, 59 and/or 61 codon. Mutant forms of H-Ras protein is continuously involved in signal transduction for cell growth and proliferation through interaction of downstream regulated protein Raf. The analysis of mutated H-Ras p21 with nine compounds resulted in enormous interactions with many hydrogen bonds and least binding energy. Introduction Emblica officinalis is a medicinal plant and medicinal properties (Krishnaveni and commonly called as Amla (or) Indian Mirunalini., 2010). It indicate a strong gooseberry belongs to Euphorbiace ae cytotoxic action of P.emblica against cancer family. Emblica officinalis gaertn cell). Amla is rich in fibre, carbohydrate, (Phyllanthus emblica linn. Amla, Indian iron and is reported as the richest sourse of gooseberry), is widely used for medicinal vitamin-c (Singh et al., 2011).The raw fruits purpose, usually from this plant, fresh, dried of P.emblica is used for a wide variety of fruits are used. The P.emblica fruits are the human ailments including cancer. P.emblica rich source of ascorbic acid (vitamin-c) possesses several biological effects such as which itself has well documented nutritional antibacterial activity, antifungal activity, 1 Int.J.Curr.Res.Aca.Rev.2017; Special Issue-4: 1-18 antioxidant and free scavenging activity, (RAS) virus homologue was the first insecticidal activity, larvicidal and oncogene to be described in human cancer mosquitocidal activity, anticancer and anti – (Der et al., 1982). In cancer, the most proliferative activity, hepato-protective commonly mutated member of the RAS activity, antimutagenic and wound healing superfamily include HRAS, KRAS, and activity, anti ulcerogenic activity, anti NRAS. The Ras protein are small (21 depressant activity, immuno-modulatory kilodalton) G-protein that are active with activity, anti-inflammatory activity, anti- bound GTP and inactive with bound GDP. diabetic and hypoglycemic activity, Although the GTP can self-hydrolyze, there hypolipidemic activity radioprotective is a class of enzyme termed GAPs (GTPase activity and many other activity activating protein) that facilitate this (Ngamkitidechakul et al., 2010). Many hydrolysis and terminate RAS activity. Two herbal and patent drugs have been decades later,the RAS pathway still remains formulated by the constituents of this plant one of the most investigated pathways in (Rai et al 2012). E.officinalis primarily human cancer (solit et al., 2006), including contains tannins, flavonoids, phenolic melanoma, and our current understanding compounds, saponins, terpenoids, ascorbic suggest that several possible mutation along acids, carbohydrates and many other this cascade lead to tumor-promoting compounds (Khan, 2009). Supplements of physiology. These protein bind GDP/GTP fresh amla fruit is very favorable to and possess intrinsic GTPase activity individual suffering from anemia (Kumar et allowing inactivation following signal al., 2012b). This herb has many bioactive transduction in the normal cellular compounds including apigenin,gallic acid, environment (Khosravi-f et al., 1994). ellagic acid, chebulini acid, quercetin, Activation of point mutations in the Ras is chebulagic acid, corilagin,isostrictiniin, one of the most frequent genetic alterations methylgallate, luteolin, emblicanin A, associated with human cancers (Spandidos, emblicanin B, phyllaemblicin B, et al., 1984). This mutation change a single punigluconin and pednculagin are tannins amino acid in the H-Ras protein. present in emblica officinalis(Kumar et al., Specifically, the mutation replaces the 2012a). amino acid glycine with the amino acid valine at position 12 (RasG12V) (oxford, G In the post-genomic era, our understanding 2003).The amino acid residues at position of the molecular biology of melanoma has 45,46,48 , 49,50,52 and 54, near the also increased dramatically. Melanoma is a previously identified effector region, differ form of skin cancer that emanates from in the Ras (Kitayama et al .,1989). The melanocytes, which are highly specialized in amino acid position which corresponds to the formation and transfer of melanin effector region on the H-Ras is 32-40 pigment. One growth factor pathway that (Ahmadian et al., 1997).The selection of this has garnered considerable attention in the effector region as a binding site will act as last few year has been the RAS-BRAF- potential site for docking studies. Ras is MAPK-ERK signaling cascade. Much of the know to induce activation of c-RAF-1 and attention surrounding this pathway in human MAP Kinase (or) extracellular signal melanoma focuses on the fact that in regulates kinase (ERK) (De vries-smits et virtually all cases, there is an alteration at al., 1992). Such signal transducing activities some level in the RAS signaling cascade are abolished by presence of mutations in (Haluska et al., 2006). The rat sarcoma the effector regionTYR32-TYR40 (Sigal et 2 Int.J.Curr.Res.Aca.Rev.2017; Special Issue-4: 1-18 al., 1986).Mutation in the effector region isostrictiniin, methylgallate, emblicanin A, affect neither guanine-nucleotide-binding phyllaemblicin B, pedunculagin are drawn nor GTPase activity, so the effector region is in ACD/Chemsketch and then converted to considered to be region that interacts with 3D structure and saved as Mdl mol format. the target effectors of the Ras protein Then it is converted to Pdb format for (Fujita-yoshigaki et al., 1995). In second, further docking process using Open Babel. experimental results of x-ray crystallographic and nuclear magnetic Protein structure preparation resonance (NMR) analyses have shown that the three-dimensional structure of the Ras Uniprot is a freely accessible database of protein changed upon GDP to GTP protein sequence and functional information exchange (Yamasaki et al ., 1989). BRAF may entires being derived from genome that promotes RAS-RAF-MEK-ERK sequencing project. pathway activation and melanoma (http://www.uniprot.org/).The protein proliferation. Docking is a process by which databank (PDB: http://www.rcsb.org/pdb/) one can predict the significant orientation of is the single worldwide archive of structural one molecule to a second when bound to data of biological macromolecules. each other to form a stable complex. It is mostly used for finding the binding between Today depositors to the pdb have varying the ligand and the protein. The information expertise in the techniques of x-ray crystal obtained from the docking technique can be structure determination, NMR, cryoelectron used to suggest the binding energy, free microscopy and theoretical modeling. energy and stability of complex. At present, docking technique is utilized to predict the ACD/Chemsketch tentative binding parameter of ligand – receptor complex beforehand, Molecular ACD/Chemsketch is a molecular modeling docking generates different possible adduct program used to create and modify images structures that are ranked and grouped of chemical structures. Also there is a together using scoring function in the software that allows molecules and software. Docking simulations predict molecular models displayed in two and three optimized docked conformer based upon dimensions, to understand the structure of total energy of the system. In spite of all chemical bonds and the nature of the potential approaches, functional groups. ligand chemistry (tautomerism and ionization), receptor flexibility (single Openbabel conformation of rigid receptor) and scoring function (differentiate true binding mode) Open babel is a chemical tool box designed still remained the challenge. [Shafia Mir et to speak the many languages of chemical al., 2017]. data. The molecular format convert tool (open babel) is used to convert this file into Materials and Methods the pdb format and is used during analysis. Ligand structure preparation SPDBV The 2D structure of apigenin, gallic acid, Target and template proteins have been ellagic acid, quercetin, corilagin, loaded in SPDBV—superimposed and 3 Int.J.Curr.Res.Aca.Rev.2017; Special Issue-4: 1-18 structurally aligned. The RMSD value found Structure Retrieval to be 0.90 Å and results. The three-dimensional structure of RAS was Autodock available in the PDB database. The PDB id is 2RGB
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